private bool ProcessChemstationMSDataFile(string datafilePath, DatasetFileInfo datasetFileInfo)
{
bool success;
var currentIndex = 0;
try
{
using (var reader = new ChemstationMSFileReader.clsChemstationDataMSFileReader(datafilePath))
{
datasetFileInfo.AcqTimeStart = reader.Header.AcqDate;
datasetFileInfo.AcqTimeEnd = datasetFileInfo.AcqTimeStart.AddMinutes(reader.Header.RetentionTimeMinutesEnd);
datasetFileInfo.ScanCount = reader.Header.SpectraCount;
for (var spectrumIndex = 0; spectrumIndex <= datasetFileInfo.ScanCount - 1; spectrumIndex++)
{
currentIndex = spectrumIndex;
ChemstationMSFileReader.clsSpectralRecord spectrum = null;
List <float> mzList = null;
List <int> intensityList = null;
const int msLevel = 1;
bool validSpectrum;
try
{
reader.GetSpectrum(spectrumIndex, ref spectrum);
mzList = spectrum.Mzs;
intensityList = spectrum.Intensities;
validSpectrum = true;
}
catch (Exception ex)
{
OnWarningEvent("Exception obtaining data from the MS file for spectrum index " + currentIndex + ": " + ex.Message);
validSpectrum = false;
}
if (validSpectrum)
{
var scanStatsEntry = new ScanStatsEntry
{
ScanNumber = spectrumIndex + 1,
ScanType = msLevel,
ScanTypeName = "GC-MS",
ScanFilterText = string.Empty,
ElutionTime = spectrum.RetentionTimeMinutes.ToString("0.0###"),
TotalIonIntensity = StringUtilities.ValueToString(spectrum.TIC, 1),
BasePeakIntensity = StringUtilities.ValueToString(spectrum.BasePeakAbundance, 1),
BasePeakMZ = spectrum.BasePeakMZ.ToString("0.0###"),
BasePeakSignalToNoiseRatio = "0",
IonCount = mzList.Count
};
scanStatsEntry.IonCountRaw = scanStatsEntry.IonCount;
mDatasetStatsSummarizer.AddDatasetScan(scanStatsEntry);
if (mSaveTICAndBPI)
{
mTICAndBPIPlot.AddData(scanStatsEntry.ScanNumber, msLevel, spectrum.RetentionTimeMinutes, spectrum.BasePeakAbundance, spectrum.TIC);
if (mzList.Count > 0)
{
var ionsMZ = new double[mzList.Count];
var ionsIntensity = new double[mzList.Count];
for (var index = 0; index <= mzList.Count - 1; index++)
{
ionsMZ[index] = mzList[index];
ionsIntensity[index] = intensityList[index];
}
mLCMS2DPlot.AddScan(scanStatsEntry.ScanNumber, msLevel, spectrum.RetentionTimeMinutes, ionsMZ.Length, ionsMZ, ionsIntensity);
}
}
if (mCheckCentroidingStatus)
{
var mzDoubles = new List <double>(mzList.Count);
mzDoubles.AddRange(mzList.Select(ion => (double)ion));
mDatasetStatsSummarizer.ClassifySpectrum(mzDoubles, msLevel, "Scan " + scanStatsEntry.ScanNumber);
}
}
}
}
success = true;
}
catch (Exception ex)
{
// Exception reading file
OnWarningEvent("Exception reading data from the MS file at spectrum index " + currentIndex + ": " + ex.Message);
success = false;
}
return(success);
}
private bool ProcessChemstationMSDataFile(string strDatafilePath, clsDatasetFileInfo datasetFileInfo)
{
bool blnSuccess;
var intCurrentIndex = 0;
try {
using (var oReader = new ChemstationMSFileReader.clsChemstationDataMSFileReader(strDatafilePath)) {
datasetFileInfo.AcqTimeStart = oReader.Header.AcqDate;
datasetFileInfo.AcqTimeEnd = datasetFileInfo.AcqTimeStart.AddMinutes(oReader.Header.RetentionTimeMinutesEnd);
datasetFileInfo.ScanCount = oReader.Header.SpectraCount;
for (var intSpectrumIndex = 0; intSpectrumIndex <= datasetFileInfo.ScanCount - 1; intSpectrumIndex++)
{
intCurrentIndex = intSpectrumIndex;
ChemstationMSFileReader.clsSpectralRecord oSpectrum = null;
List <float> lstMZs = null;
List <Int32> lstIntensities = null;
const int intMSLevel = 1;
bool blnValidSpectrum;
try {
oReader.GetSpectrum(intSpectrumIndex, ref oSpectrum);
lstMZs = oSpectrum.Mzs;
lstIntensities = oSpectrum.Intensities;
blnValidSpectrum = true;
} catch (Exception ex) {
OnWarningEvent("Exception obtaining data from the MS file for spectrum index " + intCurrentIndex + ": " + ex.Message);
blnValidSpectrum = false;
}
if (blnValidSpectrum)
{
var objScanStatsEntry = new clsScanStatsEntry
{
ScanNumber = intSpectrumIndex + 1,
ScanType = intMSLevel,
ScanTypeName = "GC-MS",
ScanFilterText = "",
ElutionTime = oSpectrum.RetentionTimeMinutes.ToString("0.0###"),
TotalIonIntensity = StringUtilities.ValueToString(oSpectrum.TIC, 1),
BasePeakIntensity = StringUtilities.ValueToString(oSpectrum.BasePeakAbundance, 1),
BasePeakMZ = oSpectrum.BasePeakMZ.ToString("0.0###"),
BasePeakSignalToNoiseRatio = "0",
IonCount = lstMZs.Count
};
objScanStatsEntry.IonCountRaw = objScanStatsEntry.IonCount;
mDatasetStatsSummarizer.AddDatasetScan(objScanStatsEntry);
if (mSaveTICAndBPI)
{
mTICandBPIPlot.AddData(objScanStatsEntry.ScanNumber, intMSLevel, oSpectrum.RetentionTimeMinutes, oSpectrum.BasePeakAbundance, oSpectrum.TIC);
if (lstMZs.Count > 0)
{
var dblIonsMZ = new double[lstMZs.Count];
var dblIonsIntensity = new double[lstMZs.Count];
for (var intIndex = 0; intIndex <= lstMZs.Count - 1; intIndex++)
{
dblIonsMZ[intIndex] = lstMZs[intIndex];
dblIonsIntensity[intIndex] = lstIntensities[intIndex];
}
mLCMS2DPlot.AddScan(objScanStatsEntry.ScanNumber, intMSLevel, oSpectrum.RetentionTimeMinutes, dblIonsMZ.Length, dblIonsMZ, dblIonsIntensity);
}
}
if (mCheckCentroidingStatus)
{
var lstMzDoubles = new List <double>(lstMZs.Count);
lstMzDoubles.AddRange(lstMZs.Select(ion => (double)ion));
mDatasetStatsSummarizer.ClassifySpectrum(lstMzDoubles, intMSLevel);
}
}
}
}
blnSuccess = true;
} catch (Exception ex) {
// Exception reading file
OnWarningEvent("Exception reading data from the MS file at spectrum index " + intCurrentIndex + ": " + ex.Message);
blnSuccess = false;
}
return(blnSuccess);
}
